Test: linux.gcc.cxx11thread.serialization.build.debug 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20701」
Test files: 「file-system-view」 「file-list-view」
Daemon: hojo-3     Started at: 2025-04-01 14:50:14     Run time: 0:02:02      State: failed


Running: /home/benchmark/prefix/hojo-3/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=gcc extras=cxx11thread,serialization -j24 scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Number of option files updated: 0 Total 4710 options. Updating submodules needed for compilation. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/LigandDiscoverySearch.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/motifs/LigandDiscoverySearch.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/protein_grid/ProteinGrid.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/protein_grid/ProteinGrid.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/movers/DisplayPoseLabelsMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/DisplayPoseLabelsMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/movers/LabelPoseFromResidueSelectorMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/LabelPoseFromResidueSelectorMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/movers/ReleaseConstraintFromResidueMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/ReleaseConstraintFromResidueMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/movers/SplitAndMixPoseMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/movers/ResidueLabelsToPymolSelectionMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/ResidueLabelsToPymolSelectionMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/movers/SavePDBInfoMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/SavePDBInfoMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/utils/utils.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/utils/utils.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/utils/Nub.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/utils/Nub.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/fold_from_loops/NubInitioMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/NubInitioMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/anchored_design/Anchor.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/anchored_design/Anchor.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/anchored_design/AnchorMovers.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/anchored_design/AnchorMovers.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/anchored_design/AnchorMoversData.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/anchored_design/AnchorMoversData.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/DesignProteinBackboneAroundDNA.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DesignProteinBackboneAroundDNA.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/DnaChains.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaChains.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/DnaInterfaceFinder.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaInterfaceFinder.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/DnaInterfaceMinMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaInterfaceMinMover.cc In file included from src/protocols/protein_grid/ProteinGrid.cc:13:0: src/protocols/protein_grid/ProteinGrid.hh:186:7: error: expected ';' at end of member declaration bool using_sub_area_ ^ g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/DnaInterfaceMultiStateDesign.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaInterfaceMultiStateDesign.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/DnaInterfacePacker.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaInterfacePacker.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/DNAParameters.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DNAParameters.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/PDBOutput.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/PDBOutput.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/RestrictDesignToProteinDNAInterface.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/RestrictDesignToProteinDNAInterface.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/RotamerDNAHBondFilter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/RotamerDNAHBondFilter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/SeparateDnaFromNonDna.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/SeparateDnaFromNonDna.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/util.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/util.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/dna/WatsonCrickRotamerCouplings.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/WatsonCrickRotamerCouplings.cc src/protocols/protein_grid/ProteinGrid.cc: In member function 'void protocols::protein_grid::ProteinGrid::initialize()': src/protocols/protein_grid/ProteinGrid.cc:224:25: error: 'option' was not declared in this scope print_whole_matrix_ = option[ OptionKeys::protein_grid::output_whole_matrix ](); ^ src/protocols/protein_grid/ProteinGrid.cc:224:25: note: suggested alternative: In file included from src/protocols/protein_grid/ProteinGrid.cc:31:0: src/basic/options/option.hh:56:25: note: 'basic::options::option' extern OptionCollection option; ^ src/protocols/protein_grid/ProteinGrid.cc:224:33: error: 'OptionKeys' has not been declared print_whole_matrix_ = option[ OptionKeys::protein_grid::output_whole_matrix ](); ^ src/protocols/protein_grid/ProteinGrid.cc:225:32: error: 'OptionKeys' has not been declared print_empty_space_ = option[ OptionKeys::protein_grid::output_empty_space ](); ^ src/protocols/protein_grid/ProteinGrid.cc: In member function 'void protocols::protein_grid::ProteinGrid::placed_ligand_space_fill_analysis(core::conformation::ResidueOP)': src/protocols/protein_grid/ProteinGrid.cc:648:55: error: 'res_num' was not declared in this scope core::Real atom_lj_radius = working_pose_->residue(res_num).atom_type(atom_num).lj_radius(); ^ src/protocols/protein_grid/ProteinGrid.cc:648:74: error: 'atom_num' was not declared in this scope core::Real atom_lj_radius = working_pose_->residue(res_num).atom_type(atom_num).lj_radius(); ^ src/protocols/protein_grid/ProteinGrid.cc: In member function 'core::pose::Pose protocols::protein_grid::ProteinGrid::export_protein_matrix_to_pose()': src/protocols/protein_grid/ProteinGrid.cc:863:11: error: could not convert '((protocols::protein_grid::ProteinGrid*)this)->protocols::protein_grid::ProteinGrid::working_pose_' from 'core::pose::PoseOP {aka std::shared_ptr<core::pose::Pose>}' to 'core::pose::Pose' return working_pose_; ^ src/protocols/protein_grid/ProteinGrid.cc:920:3: error: 'pose' has not been declared pose::Pose matrix_pose; ^ src/protocols/protein_grid/ProteinGrid.cc:920:14: error: expected ';' before 'matrix_pose' pose::Pose matrix_pose; ^ src/protocols/protein_grid/ProteinGrid.cc:964:10: error: 'matrix_pose' was not declared in this scope return matrix_pose; ^ src/protocols/protein_grid/ProteinGrid.cc:914:14: error: unused variable 'atom_counter' [-Werror=unused-variable] core::Size atom_counter = 0; ^ src/protocols/protein_grid/ProteinGrid.cc:917:14: error: unused variable 'total_atom_counter' [-Werror=unused-variable] core::Size total_atom_counter = 0; ^ src/protocols/protein_grid/ProteinGrid.cc: In function 'void protocols::protein_grid::export_protein_matrix_to_pdb(std::string)': src/protocols/protein_grid/ProteinGrid.cc:972:83: error: 'fullness_ratio_' was not declared in this scope std::string matrix_pdb_name = pdb_name_prefix + "_WholeRatio_" + std::to_string(fullness_ratio_); ^ src/protocols/protein_grid/ProteinGrid.cc:975:6: error: 'using_sub_area_' was not declared in this scope if(using_sub_area_) ^ src/protocols/protein_grid/ProteinGrid.cc:977:70: error: 'sub_fullness_ratio_' was not declared in this scope matrix_pdb_name = matrix_pdb_name + "_SubRatio_" + std::to_string(sub_fullness_ratio_); ^ src/protocols/protein_grid/ProteinGrid.cc:986:3: error: 'pose' has not been declared pose::Pose matrix_pose = export_protein_matrix_to_pose(); ^ src/protocols/protein_grid/ProteinGrid.cc:986:14: error: expected ';' before 'matrix_pose' pose::Pose matrix_pose = export_protein_matrix_to_pose(); ^ src/protocols/protein_grid/ProteinGrid.cc:989:3: error: 'matrix_pose' was not declared in this scope matrix_pose.dump_pdb(matrix_pdb_name); ^ src/protocols/protein_grid/ProteinGrid.cc:992:3: error: 'add_comment' is not a member of 'core::pose' core::pose::add_comment(*working_pose_, "Corresponding space fill matrix file:", matrix_pdb_name); ^ src/protocols/protein_grid/ProteinGrid.cc:992:28: error: 'working_pose_' was not declared in this scope core::pose::add_comment(*working_pose_, "Corresponding space fill matrix file:", matrix_pdb_name); ^ g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/grafting/AnchoredGraftMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/grafting/AnchoredGraftMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/grafting/CCDEndsGraftMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/grafting/CCDEndsGraftMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/grafting/GraftMoverBase.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/grafting/GraftMoverBase.cc src/protocols/protein_grid/ProteinGrid.cc: In member function 'core::pose::Pose protocols::protein_grid::ProteinGrid::export_protein_matrix_to_pose()': src/protocols/protein_grid/ProteinGrid.cc:965:2: error: control reaches end of non-void function [-Werror=return-type] } ^ cc1plus: all warnings being treated as errors In file included from src/protocols/motifs/LigandDiscoverySearch.cc:136:0: src/protocols/protein_grid/ProteinGrid.hh:186:7: error: expected ';' at end of member declaration bool using_sub_area_ ^ g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/grafting/util.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/grafting/util.cc scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/protein_grid/ProteinGrid.os] Error 1 scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/LigandDiscoverySearch.os] Error 1 scons: building terminated because of errors.
{}